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3h66

Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms

Method: X-RAY DIFFRACTION Dmax: 91.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein phosphatase 5

Homo sapiens

UniProt P53041

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 176–490 Fragment：Catalytic domain, residues 176-490 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K Resolution 2.59 Å R-free 0.291
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 176–490 Fragment：Catalytic domain, residues 176-490 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K Resolution 2.59 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3H66 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A17 TETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5 Deposited 1997-12-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 16–181（166 aa） Fragment：PROTEIN INTERACTING DOMAIN
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.8 M AMMONIUM SULFATE, 4% MPD, 100 MM HEPES PH 7.5, 2 MM DTT
Resolution 2.45 Å R-free 0.298
1A17 TETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5 Deposited 1997-12-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 16–181（166 aa） Fragment：PROTEIN INTERACTING DOMAIN
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.8 M AMMONIUM SULFATE, 4% MPD, 100 MM HEPES PH 7.5, 2 MM DTT
Resolution 2.45 Å R-free 0.298
1S95 Structure of serine/threonine protein phosphatase 5 Deposited 2004-02-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 169–499（331 aa） Fragment：catalytic domain
Not recorded MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2-methyl,2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.209
1S95 Structure of serine/threonine protein phosphatase 5 Deposited 2004-02-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 169–499（331 aa） Fragment：catalytic domain
Not recorded MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2-methyl,2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.209
1S95 Structure of serine/threonine protein phosphatase 5 Deposited 2004-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 169–499（331 aa） Fragment：catalytic domain
Chain B 169–499（331 aa） Fragment：catalytic domain
Not recorded MN MANGANESE (II) ION × 4 PO4 PHOSPHATE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2-methyl,2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.209
1WAO PP5 structure Deposited 2004-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain 1 23–499（477 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions PEG 6K 10%
Resolution 2.90 Å R-free 0.290
1WAO PP5 structure Deposited 2004-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain 2 23–499（477 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions PEG 6K 10%
Resolution 2.90 Å R-free 0.290
1WAO PP5 structure Deposited 2004-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain 3 23–499（477 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions PEG 6K 10%
Resolution 2.90 Å R-free 0.290
1WAO PP5 structure Deposited 2004-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain 4 23–499（477 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions PEG 6K 10%
Resolution 2.90 Å R-free 0.290
2BUG Solution structure of the TPR domain from Protein phosphatase 5 in complex with Hsp90 derived peptide Deposited 2005-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–147（129 aa） Fragment：TETRATRICOPEPTIDE DOMAIN, RESIDUES 19-147
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 55；Pressure 1.0
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 55；Pressure 1.0
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 55；Pressure 1.0
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 55；Pressure 1.0
NMR sample composition 50MM MES, 5MM DTT (PH6.0) 10%D2O, 90% H2O
Resolution not provided
3H60 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Mn2+ atoms Deposited 2009-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, MPD 40%, PEG MME 5000 20%, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.00 Å R-free 0.219
3H60 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Mn2+ atoms Deposited 2009-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, MPD 40%, PEG MME 5000 20%, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.00 Å R-free 0.219
3H61 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with norcantharidin (which is present in the structure in the hydrolyzed form) Deposited 2009-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 ENL (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HC, 40% MPD, 20% PEG MME 5000 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.45 Å R-free 0.194
3H61 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with norcantharidin (which is present in the structure in the hydrolyzed form) Deposited 2009-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 ENL (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HC, 40% MPD, 20% PEG MME 5000 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.45 Å R-free 0.194
3H62 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms complexed with cantharidic acid Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.40 Å R-free 0.204
3H62 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms complexed with cantharidic acid Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.40 Å R-free 0.204
3H63 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form) Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.30 Å R-free 0.191
3H63 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form) Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.30 Å R-free 0.191
3H64 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms complexed with endothall Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 ENL (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.90 Å R-free 0.237
3H64 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms complexed with endothall Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded MN MANGANESE (II) ION × 2 ENL (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.90 Å R-free 0.237
3H67 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms complexed with cantharidic acid Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded ZN ZINC ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.65 Å R-free 0.231
3H67 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms complexed with cantharidic acid Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded ZN ZINC ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.65 Å R-free 0.231
3H68 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form) Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded ZN ZINC ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.50 Å R-free 0.232
3H68 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form) Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded ZN ZINC ION × 2 NHC (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.50 Å R-free 0.232
3H69 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms complexed with endothall Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded ZN ZINC ION × 2 ENL (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.10 Å R-free 0.227
3H69 Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms complexed with endothall Deposited 2009-04-23 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 176–490（315 aa） Fragment：Catalytic domain, residues 176-490
Not recorded ZN ZINC ION × 2 ENL (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.10 Å R-free 0.227
4ZVZ Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid Deposited 2015-05-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 169–499（331 aa） Fragment：UNP residues 169-499
Not recorded MN MANGANESE (II) ION × 2 4TF (1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；25% MPD, 6% PEG, 10 mM Tris, pH 8.0
Resolution 2.00 Å R-free 0.235
4ZVZ Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid Deposited 2015-05-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 169–499（331 aa） Fragment：UNP residues 169-499
Not recorded MN MANGANESE (II) ION × 2 4TF (1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；25% MPD, 6% PEG, 10 mM Tris, pH 8.0
Resolution 2.00 Å R-free 0.235
4ZVZ Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid Deposited 2015-05-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 169–499（331 aa） Fragment：UNP residues 169-499
Not recorded MN MANGANESE (II) ION × 2 4TF (1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；25% MPD, 6% PEG, 10 mM Tris, pH 8.0
Resolution 2.00 Å R-free 0.235
4ZVZ Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid Deposited 2015-05-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 169–499（331 aa） Fragment：UNP residues 169-499
Not recorded MN MANGANESE (II) ION × 2 4TF (1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；25% MPD, 6% PEG, 10 mM Tris, pH 8.0
Resolution 2.00 Å R-free 0.235
4ZX2 Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid Deposited 2015-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 169–499（331 aa） Fragment：UNP residues 169-499
Not recorded MN MANGANESE (II) ION × 2 4TE (1S,2R,3S,4R,5S)-5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；25% MPD, 6% PEG, 10 mM Tris, pH 8.0
Resolution 1.23 Å R-free 0.175
5HPE Phosphatase domain of PP5 bound to a phosphomimetic Cdc37 substrate peptide Deposited 2016-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 175–499（325 aa）
Mutation：S13E MN MANGANESE (II) ION × 2 NCO COBALT HEXAMMINE(III) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；18% PEG, 8% ethylene glycol, 0.1M Hepes pH 7.5, 20mM hexamine cobolt chloride
Resolution 2.27 Å R-free 0.236
5UI1 Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole inhibitor Deposited 2017-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 169–499（331 aa）
Not recorded MN MANGANESE (II) ION × 2 8D4 5-phenyl-1H-1,2,3-triazole-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；20-26% MPD, 4-8% PEG5000MME, 1 mM Manganese chloride, 10 mM Tris
Resolution 1.96 Å R-free 0.246
5UI1 Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole inhibitor Deposited 2017-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 169–499（331 aa）
Not recorded MN MANGANESE (II) ION × 2 8D4 5-phenyl-1H-1,2,3-triazole-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；20-26% MPD, 4-8% PEG5000MME, 1 mM Manganese chloride, 10 mM Tris
Resolution 1.96 Å R-free 0.246
5UI1 Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole inhibitor Deposited 2017-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 169–499（331 aa）
Not recorded MN MANGANESE (II) ION × 2 8D4 5-phenyl-1H-1,2,3-triazole-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；20-26% MPD, 4-8% PEG5000MME, 1 mM Manganese chloride, 10 mM Tris
Resolution 1.96 Å R-free 0.246
5UI1 Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole inhibitor Deposited 2017-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 169–499（331 aa）
Not recorded MN MANGANESE (II) ION × 2 8D4 5-phenyl-1H-1,2,3-triazole-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；20-26% MPD, 4-8% PEG5000MME, 1 mM Manganese chloride, 10 mM Tris
Resolution 1.96 Å R-free 0.246
5WG8 Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density Deposited 2017-07-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 169–499（331 aa） Fragment：UNP residues 169-499
Not recorded MN MANGANESE (II) ION × 2 LB1 (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289.15 K；10 mM Tris-HCl pH 8.0, 35% 2-methyl-2,4-pentanediol, and 10% polyethylene glycol methyl ether 5000
Resolution 1.65 Å R-free 0.196
7ZR5 CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(closed) complex Deposited 2022-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 17–499（483 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ZR6 CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(open) complex Deposited 2022-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 17–499（483 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8GAE Hsp90 provides platform for CRaf dephosphorylation by PP5 Deposited 2023-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–499（499 aa）
Mutation：H304A K POTASSIUM ION × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3UL OF SAMPLE 10C 100% HUMIDITY 30S WAIT TIME 3S BLOT TIME -2 BLOT FORCE
Resolution 3.30 Å
8GFT Hsp90 provides platform for CRaf dephosphorylation by PP5 Deposited 2023-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–499（499 aa）
Mutation：H304A ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3uL OF SAMPLE, 10C, 100% HUMIDITY, 30S WAIT TIME, 3S BLOT TIME, -2 BLOT FORCE
Resolution 3.80 Å

21 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPP5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–315； UniProt 176–490 Author chain B； PDBConstruct 1–315； UniProt 176–490

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3h66

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3h66
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3h66
Deposition date deposition_date2009-04-23
Structure title titleCatalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms
Keywords keywordsmetalloenzyme, phosphatase, Cytoplasm, Hydrolase, Iron, Manganese, Metal-binding, Nucleus, Protein phosphatase, TPR repeat; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.89 Å
Radius of gyration Rg (electron density) rg_electron28.46 Å
Forward intensity I(0) i083416100.00
Molecular weight molecular_weight72027.0 kDa
Excluded volume excluded_volume90025 ų
Envelope volume envelope_volume106460 ų
Hydration-shell volume shell_volume31119 ų
Envelope diameter envelope_diameter96.8 Å
Shell Rg shell_rg35.81 Å
Envelope Rg envelope_rg28.37 Å
Shape Rg shape_rg28.46 Å
Total Rg total_rg29.18 Å
Total atoms total_atoms5060
Residues n_residues630
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax91.8 Å
Rg (real space) rg_real28.92 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real8.3420e+07
I(0) uncertainty (real space) i0_real_error1.2340e+06
Rg (reciprocal space) rg_reciprocal28.91 Å
I(0) (reciprocal space) i0_reciprocal83420000.0000
Solution quality estimate total_estimate0.8946
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.323
Kurtosis Kurtosis kurtosis-0.603
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21540000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.968
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3h66a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd3h66b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id3h66A00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id3h66B00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
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8. Citations (1)

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9. Files and Curves (10)